LAMMPS (8 Feb 2023)
Processor partition = 1
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
variable ibead uloop 8 pad

units           real
neigh_modify    delay 2 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic

pair_style      lj/charmm/coul/long 11 12
pair_modify     mix arithmetic
kspace_style    pppm 1e-4

read_data system.data
Reading data file ...
  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  8674 atoms
  reading velocities ...
  8674 velocities
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  18 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  5869 bonds
  reading angles ...
  3264 angles
  reading dihedrals ...
  708 dihedrals
  reading impropers ...
  38 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     9 = max # of 1-3 neighbors
    17 = max # of 1-4 neighbors
    21 = max # of special neighbors
  special bonds CPU = 0.004 seconds
  read_data CPU = 0.139 seconds
#read_restart    system_${ibead}.rest1
special_bonds   charmm

fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0

thermo          10
thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
timestep        0.08

# restart         100 system_${ibead}.rest1 system_${ibead}.rest2

group prot id <= 256
256 atoms in group prot
# dump 1 prot dcd 100 prot_${ibead}.dcd

run             200
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.22071363
  grid = 20 20 20
  stencil order = 5
  estimated absolute RMS force accuracy = 0.024910591
  estimated relative force accuracy = 7.5017505e-05
  using double precision KISS FFT
  3d grid and FFT values/proc = 15625 8000
Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 2 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
WARNING: Inconsistent image flags (src/domain.cpp:815)
Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
        10   64.17217      -26206.83      -24547.814      19.798491      300.69483     -715.39964    
        20   68.220475     -26516.716     -24753.042      40.042407      319.66418     -514.11207    
        30   57.966715     -26566.219     -25067.631      92.36071       271.61761      32.199121    
        40   49.627434     -26115.147     -24832.15       156.77313      232.54181      589.56751    
        50   50.238512     -24830.72      -23531.926      251.81147      235.40517      1098.4708    
        60   56.338925     -22753.456     -21296.951      361.53524      263.99019      1897.4199    
        70   54.380851     -19964.7       -18558.815      512.1854       254.81514      2327.9231    
        80   56.718808     -16822.195     -15355.868      692.48978      265.77022      2784.4839    
        90   57.350586     -13726.44      -12243.78       926.0914       268.73058      3260.3863    
       100   57.262365     -11280.793     -9800.4136      1186.0078      268.3172       3554.7754    
       110   58.507688     -9681.3843     -8168.8105      1483.328       274.15247      3368.3688    
       120   58.690757     -9008.7198     -7491.4132      1803.3617      275.01029      2974.5497    
       130   58.623212     -9097.3273     -7581.7669      2143.6544      274.69379      2535.9822    
       140   59.453502     -9689.6967     -8152.6711      2490.8635      278.58432      1947.3155    
       150   59.231787     -10601.929     -9070.635       2837.9543      277.54542      1774.9432    
       160   58.39319      -11413.85      -9904.2362      3183.3024      273.61596      1744.3579    
       170   60.201493     -12074.462     -10518.099      3515.6508      282.08922      1744.1497    
       180   59.592955     -12415.79      -10875.16       3827.6991      279.23776      1935.0884    
       190   59.698333     -12625.161     -11081.806      4120.4275      279.73154      1962.5444    
       200   59.87495      -12794.677     -11246.756      4387.202       280.55912      1854.7836    
Loop time of 35.3334 on 1 procs for 200 steps with 8674 atoms

Performance: 0.039 ns/day, 613.427 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
97.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 27.948     | 27.948     | 27.948     |   0.0 | 79.10
Bond    | 0.12842    | 0.12842    | 0.12842    |   0.0 |  0.36
Kspace  | 2.4577     | 2.4577     | 2.4577     |   0.0 |  6.96
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.11986    | 0.11986    | 0.11986    |   0.0 |  0.34
Output  | 0.0021166  | 0.0021166  | 0.0021166  |   0.0 |  0.01
Modify  | 4.617      | 4.617      | 4.617      |   0.0 | 13.07
Other   |            | 0.06042    |            |       |  0.17

Nlocal:           8674 ave        8674 max        8674 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          27366 ave       27366 max       27366 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 4485849
Ave neighs/atom = 517.16036
Ave special neighs/atom = 2.2573207
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:35
